PDBsum entry 1elq

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
Jmol PyMol
Protein chains
381 a.a. *
PLP ×2
__K ×2
Waters ×706
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Crystal structure of the cystinE C-s lyasE C-des
Structure: L-cysteine/l-cystinE C-s lyase. Chain: a, b. Fragment: 11 residues of the wt-n-terminus replaced by octa engineered: yes. Mutation: yes. Other_details: n-terminal modified c-des retains full catal activity
Source: Synechocystis sp.. Organism_taxid: 1147. Strain: pcc 6714. Expressed in: bacteria. Expression_system_taxid: 2
Biol. unit: Dimer (from PQS)
1.80Å     R-factor:   0.198     R-free:   0.249
Authors: T.Clausen,J.T.Kaiser,C.Steegborn,R.Huber,D.Kessler
Key ref:
T.Clausen et al. (2000). Crystal structure of the cystine C-S lyase from Synechocystis: stabilization of cysteine persulfide for FeS cluster biosynthesis. Proc Natl Acad Sci U S A, 97, 3856-3861. PubMed id: 10760256 DOI: 10.1073/pnas.97.8.3856
14-Mar-00     Release date:   19-Apr-00    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q9ZHG9  (Q9ZHG9_SYNY4) -  L-cysteine/cystine lyase C-DES
393 a.a.
381 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     lyase activity     1 term  


DOI no: 10.1073/pnas.97.8.3856 Proc Natl Acad Sci U S A 97:3856-3861 (2000)
PubMed id: 10760256  
Crystal structure of the cystine C-S lyase from Synechocystis: stabilization of cysteine persulfide for FeS cluster biosynthesis.
T.Clausen, J.T.Kaiser, C.Steegborn, R.Huber, D.Kessler.
FeS clusters are versatile cofactors of a variety of proteins, but the mechanisms of their biosynthesis are still unknown. The cystine C-S lyase from Synechocystis has been identified as a participant in ferredoxin FeS cluster formation. Herein, we report on the crystal structure of the lyase and of a complex with the reaction products of cystine cleavage at 1.8- and 1.55-A resolution, respectively. The sulfur-containing product was unequivocally identified as cysteine persulfide. The reactive persulfide group is fixed by a hydrogen bond to His-114 in the center of a hydrophobic pocket and is thereby shielded from the solvent. Binding and stabilization of the cysteine persulfide represent an alternative to the generation of a protein-bound persulfide by NifS-like proteins and point to the general importance of persulfidic compounds for FeS cluster assembly.
  Selected figure(s)  
Figure 1.
Fig. 1. Overall fold of C-DES. (A) Stereo ribbon drawing of the homodimer showing the PLP covalently bound to Lys-223 (color-coded by atom type) and the K+ ion (red) rigidifying a solvent-exposed loop in ball-and-stick mode. In the upper monomer, the course of the polypeptide chain is illustrated by a color ramp starting at the N terminus with blue and ending at the C terminus with red. Secondary structure elements, which are substantial for dimer stabilization, are labeled in red. The lower monomer is colored by secondary structure with the nomenclature of the two central -sheets given. (B) Stereo representation of the surface of the active dimer color-coded by the monomers (white and orange). The product of cystine cleavage, cysteine persulfide, is shown in a ball-and-stick representation to illustrate the large dimensions of the active-site funnel. Note the enclosure of the terminal persulfidic group by C-DES to shield it from solvent. Fig. 1A was produced with MOLSCRIPT (23) and RASTER3D (24); all other figures were created with DINO (
Figure 3.
Fig. 3. Proposed reaction mechanism for C-DES. The colors used are green, PLP; red, cystine; black, apoprotein. Hydrogen bonds are indicated by dashed lines and hydrophobic interactions by curly lines.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21081698 M.Koutmos, O.Kabil, J.L.Smith, and R.Banerjee (2010).
Structural basis for substrate activation and regulation by cystathionine beta-synthase (CBS) domains in cystathionine {beta}-synthase.
  Proc Natl Acad Sci U S A, 107, 20958-20963.
PDB codes: 3pc2 3pc3 3pc4
20164179 R.Omi, S.Kurokawa, H.Mihara, H.Hayashi, M.Goto, I.Miyahara, T.Kurihara, K.Hirotsu, and N.Esaki (2010).
Reaction mechanism and molecular basis for selenium/sulfur discrimination of selenocysteine lyase.
  J Biol Chem, 285, 12133-12139.
PDB codes: 3a9x 3a9y 3a9z
17064282 D.Kessler (2006).
Enzymatic activation of sulfur for incorporation into biomolecules in prokaryotes.
  FEMS Microbiol Rev, 30, 825-840.  
15952888 D.C.Johnson, D.R.Dean, A.D.Smith, and M.K.Johnson (2005).
Structure, function, and formation of biological iron-sulfur clusters.
  Annu Rev Biochem, 74, 247-281.  
16328784 D.Kessler, and J.Papenbrock (2005).
Iron-sulfur cluster biosynthesis in photosynthetic organisms.
  Photosynth Res, 86, 391-407.  
16204001 N.Numoto, T.Nakagawa, A.Kita, Y.Sasayama, Y.Fukumori, and K.Miki (2005).
Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi.
  Proc Natl Acad Sci U S A, 102, 14521-14526.
PDB codes: 2d2m 2d2n
15688436 R.Prabhakar, K.Morokuma, and D.G.Musaev (2005).
A comparative study of various computational approaches in calculating the structure of pyridoxal 5'-phosphate (PLP)-dependent beta-lyase protein. The importance of protein environment.
  J Comput Chem, 26, 443-446.  
15498941 A.Paiardini, F.Bossa, and S.Pascarella (2004).
Evolutionarily conserved regions and hydrophobic contacts at the superfamily level: The case of the fold-type I, pyridoxal-5'-phosphate-dependent enzymes.
  Protein Sci, 13, 2992-3005.  
14596599 T.Yamada, J.Komoto, Y.Takata, H.Ogawa, H.C.Pitot, and F.Takusagawa (2003).
Crystal structure of serine dehydratase from rat liver.
  Biochemistry, 42, 12854-12865.
PDB codes: 1pwe 1pwh
12970193 U.Mühlenhoff, J.Gerber, N.Richhardt, and R.Lill (2003).
Components involved in assembly and dislocation of iron-sulfur clusters on the scaffold protein Isu1p.
  EMBO J, 22, 4815-4825.  
12022883 E.A.James, S.P.Gygi, M.L.Adams, R.H.Pierce, N.Fausto, R.H.Aebersold, S.D.Nelson, and S.A.Bruschi (2002).
Mitochondrial aconitase modification, functional inhibition, and evidence for a supramolecular complex of the TCA cycle by the renal toxicant S-(1,1,2,2-tetrafluoroethyl)-L-cysteine.
  Biochemistry, 41, 6789-6797.  
12119031 M.Bertoldi, B.Cellini, T.Clausen, and C.B.Voltattorni (2002).
Spectroscopic and kinetic analyses reveal the pyridoxal 5'-phosphate binding mode and the catalytic features of Treponema denticola cystalysin.
  Biochemistry, 41, 9153-9164.  
11555280 K.E.Ellis, B.Clough, J.W.Saldanha, and R.J.Wilson (2001).
Nifs and Sufs in malaria.
  Mol Microbiol, 41, 973-981.  
10971575 H.Beinert (2000).
A tribute to sulfur.
  Eur J Biochem, 267, 5657-5664.  
11106419 M.Hans, W.Buckel, and E.Bill (2000).
The iron-sulfur clusters in 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. Biochemical and spectroscopic investigations.
  Eur J Biochem, 267, 7082-7093.  
10916152 R.Lill, and G.Kispal (2000).
Maturation of cellular Fe-S proteins: an essential function of mitochondria.
  Trends Biochem Sci, 25, 352-356.  
11004453 U.Mühlenhoff, and R.Lill (2000).
Biogenesis of iron-sulfur proteins in eukaryotes: a novel task of mitochondria that is inherited from bacteria.
  Biochim Biophys Acta, 1459, 370-382.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.